﻿/* 
* Copyright (c) 2010, The University of Texas at Austin
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, 
* are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, 
* this list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright notice, 
* this list of conditions and the following disclaimer in the documentation and/or other materials 
* provided with the distribution.
*
* Neither the name of The University of Texas at Austin nor the names of its contributors may be 
* used to endorse or promote products derived from this software without specific prior written 
* permission.
* 
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR 
* IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND 
* FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS 
* BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
* PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF 
* THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/

using System.Collections.Generic;
using System.Linq;
using Bio.Data.Interfaces;

namespace Bio.Data.Providers.Structure
{
    public class RNASecondaryStructureExtent : IStructureExtentBioEntity
    {
        #region IStructureExtentBioEntity Members

        public int ID 
        {
            get { return _id; }
        }

        public int Ordinal
        {
            get { return _ordinal; }
        }

        public StructureExtentType Type
        {
            get { return _type; }
        }

        public int StartIndex
        {
            get { return _startIndex; }
        }

        public int EndIndex
        {
            get { return _endIndex; }
        }

        public IList<IBioSymbol> Elements
        {
            get { return _sequence.SequenceData.Where((e, i) => (i >= StartIndex && i <= EndIndex)).ToList(); }
        }

        #endregion

        public RNASecondaryStructureExtent(IBioSequence sequence,
            int id, int ordinal, StructureExtentType type, int startIndex, int endIndex)
        {
            _sequence = sequence;
            _startIndex = startIndex;
            _endIndex = endIndex;
            _id = id;
            _ordinal = ordinal;
            _type = type;
        }

        private int _startIndex;
        private int _endIndex;
        private int _ordinal;
        private int _id;
        private StructureExtentType _type;
        private IBioSequence _sequence;
    }
}
